Superman is a global hero and his powers allow him to face challenges that are bigger than Metropolis. While I would like to have a game that features missions in Metropolis (specifically at the start), I won't want to have to stay in Metropolis because that could get boring. Let me go to Gotham City and uncover secret conspiracies with Batman/Bruce Wayne. Let me fight giants, sorcerers, and gods with Wonder Woman/Diana Prince on Paradise Island. Let me visit Oa and fight alongside John Stewart and the Green Lantern Corps. Let me see the Source Wall and fight Apocalypse.
Don't weaken Superman, but give him challenges that will push his limits. Don't fill the game with mini-games or make the point of the game "holding back." Let Superman cut loose. Let him smash entire building if he has to. This may mean using some kind of Darksiders gameplay mechanic. But it should be somewhat skill-based. It would be cool if there were some escape missions that resembled racing games like "Burnout 3" but with flight. It might be helpful to have some kind of target-ting trigger like in "Zelda Ocarina of Time" to lock on to opponents in the air and fight them one-on-one. Oh, and let me use my surroundings. Let me pull out support beams in Metropolis and use them like bats. Let me use Greek Statues to bash Ares. Let me freeze Sinestro Corps Lanterns and chuck them at Red Lanterns.
It can't be all punches. Let's have Clark figure out some puzzles and solve some mysteries. He is a reporter. And there are strange new things all around the DCU.